run_samsort: Wrapper scripts for SAMtools functions
In anilchalisey/chompR: ChIP and ATAC-seq data processing pipeline

Description Usage Arguments Value Examples

run_samsort sorts alignment (SAM/BAM/CRAM) files either by position or read name using samtools sort.

run_samindex indexes sorted BAM files using samtools index.

run_samview outputs all alignments matching the flag and region filters specified in either SAM or BAM format using samtools view.

run_samflagstat uses samtools flagstat to calculate and print statistics from a BAM file. It provides counts for 13 categories of reads: total, secondary, supplementary, duplicates, mapped, paired in sequencing, read1, read2, properly paired, with itself and its mate mapped, singletons, mate mapped to a different chromosome, with mate mapped to a different chromosome with MAPQ>5.

run_samsort(file = NULL, samtools = "samtools", outformat = "BAM",
  threads = 1, memory = "768M", sortbyname = FALSE, suffix = "",
  keep = TRUE)

run_samindex(samtools = "samtools", bamfile = NULL, threads = 1)

run_samview(samtools = "samtools", file = NULL, regions = NULL,
  chrom.sizes = NULL, include.flag = NULL, exclude.flag = NULL,
  minQual = NULL, outformat = NULL, outname = NULL,
  include.header = FALSE, count = FALSE, threads = 1,
  subsample = NULL, keep.paired = TRUE, keep.proper.pair = TRUE,
  remove.unmapped = FALSE, remove.not.primary = FALSE,
  remove.duplicates = FALSE, remove.supplementary.alignment = FALSE,
  remove.mitochondrial = NULL)

run_samflagstat(bamfile = NULL, samtools = "samtools", threads = 1)

`file`	A vector of characters specifying the path to the bam files.
`samtools`	The path to samtools (if not in executable path).
`outformat`	String specifying output format: ('SAM'/'BAM'/'CRAM'). For `run_samview` this should be SAM or 'BAM' only.
`threads`	A positive integer specifying the number of sorting and compression threads
`memory`	String specifying maximum memory per thread; suffix K/M/G recognized.
`sortbyname`	Boolean. If TRUE, reads are sorted by name. If FALSE, reads are sorted by chromosome/position.
`suffix`	Suffix to add to the basename of the file e.g, _psort (for position-sorted).
`keep`	Boolean. If TRUE, the input file is kept. If FALSE, the input file is deleted after a successful sort.
`bamfile`	Vector of characters specifying the path to sorted BAM files.
`regions`	Either path to a single BED file containing regions of interest or regions defined in the format "RNAME:START[-END]".
`chrom.sizes`	Path to chromosome size file. Required if converting to SAM format and including header. If not available, then one will be generated automatically from the existing header. This is a tab-delimited text file where each line contains the reference name in the first column and length in the second column.
`include.flag`	Integer value. Include output of alignments with any bits set in this value present in the FLAG field. See https:://broadinstitute.github.io.
`exclude.flag`	Integer value. Exclude output of alignments with any bits set in this value present in the FLAG field. See https:://broadinstitute.github.io.
`minQual`	Skip alignments with MAPQ smaller than this value.
`outname`	Name for output file.
`include.header`	Boolean. If TRUE header is included. This option is only necessary if outformat = "SAM" as header always included in "BAM".
`count`	Boolean. If true, only count alignments instead of printing.
`subsample`	Float value - if set then subsampling is performed. The integer part is used to seed the random number generator and the part after the decimal sets the fraction of reads to subsample.
`keep.paired`	Boolean. If TRUE, keep paired reads only.
`keep.proper.pair`	Boolean. If TRUE, keep concordantly paired reads only.
`remove.unmapped`	Boolean. If TRUE, remove unmapped reads.
`remove.not.primary`	Boolean. If TRUE, remove reads mapped as secondary alignments.
`remove.duplicates`	Boolean. If TRUE, remove reads marked as optical or PCR duplicates.
`remove.supplementary.alignment`	Boolean. If TRUE, remove reads marked as supplementary alignment.
`remove.mitochondrial`	Character string. If set, this will remove reads mapping to the mitochondrial genome. The string should match the reference name for the mitochindrial genome in the alignment file. Examples include "ChrM", "M" and "MT".

run_samsort returns a sorted alignment file.

run_samindex returns a BAI-format index file for sorted BAM files.

run_samview returns aligned reads according to the regions and filters specified in BAM or SAM format.

run_samflagstat returns a dataframe of alignment statistics.

## Not run: 
run_samsort(file = "HB1_sample.sam", samtools = "samtools",
            outformat = "BAM", threads = (parallel::detectCores() - 1),
            memory = "1G", sortbyname = FALSE, suffix = "", keep = TRUE)


## End(Not run)

## Not run: 
run_samindex(samtools = "samtools", bamfile = "HB1_sample.bam",
threads = (parallel::detectCores() - 1))

## End(Not run)

## Not run: 
run_samview(samtools = "samtools", file = "HB1_sample.bam", regions = NULL,
chrom.sizes = NULL, include.flag = NULL, exclude.flag = NULL,
minQual = NULL, outformat = "BAM", outname = NULL, include.header = FALSE,
count = FALSE, threads = (parallel::detectCores() - 1), subsample = NULL,
keep.paired = TRUE, keep.proper.pair = TRUE, remove.unmapped = TRUE,
remove.not.primary = TRUE, remove.duplicates = TRUE,
remove.supplementary.alignment = TRUE, remove.mitochondrial = "ChrM")

## End(Not run)

## Not run: 
run_samflagstat(samtools = "samtools", threads = parallel::detectCores(),
                bamfile = "HB1_sample.bam")

## End(Not run)